Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz
Thank you very much, Hervé! On Wed, Mar 31, 2021 at 8:25 AM Hervé Pagès wrote: > Hi Stian, > > I know I know, this thread is almost 1 year old. I had s sticker hanging > around to remind me about this, and, today, I spent the entire afternoon > looking into this, found the problem, and implemented a fix. > > Long story short: On our Mac builders, the png() device was using the > "Xlib" type by default. Problem is that png(type="Xlib") does not > support semi-transparency (and this seems to be the case on all Mac and > Linux systems). I changed this to use the "cairo" type by default (this > is the default on Linux). With this change, I was finally able to run 'R > CMD build chimeraviz' successfully on the machine. > > I also found out that this problem was also breaking the srnadiff package. > > We won't see the effect of that change on today's build report, but > hopefully we will on tomorrow's report. > > Cheers, > H. > > > On 4/23/20 11:33 PM, Stian Lågstad wrote: > > Thank you very much for the help so far! > > > > On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès > <mailto:hpa...@fredhutch.org>> wrote: > > > > OK, thanks testing that. This suggests that the problem is on our > > side... sigh! I will need to dig deeper into this. > > > > Best, > > H. > > > > > > On 4/23/20 22:57, Bemis, Kylie wrote: > > > Worked for me without errors or warnings: > > > > > > kuwisdelu@Eva-02-Dash Projects % R CMD build chimeraviz > > > * checking for file ‘chimeraviz/DESCRIPTION’ ... OK > > > * preparing ‘chimeraviz’: > > > * checking DESCRIPTION meta-information ... OK > > > * installing the package to build vignettes > > > * creating vignettes ... OK > > > * checking for LF line-endings in source and make files and shell > > scripts > > > * checking for empty or unneeded directories > > > Removed empty directory ‘chimeraviz/docker’ > > > * building ‘chimeraviz_1.13.8.tar.gz’ > > > > > > kuwisdelu@Eva-02-Dash Projects % R CMD INSTALL > > chimeraviz_1.13.8.tar.gz > > > * installing to library ‘/Users/kuwisdelu/Library/R/4.0/library’ > > > * installing *source* package ‘chimeraviz’ ... > > > ** using staged installation > > > ** R > > > ** inst > > > ** byte-compile and prepare package for lazy loading > > > ** help > > > *** installing help indices > > > ** building package indices > > > ** installing vignettes > > > ** testing if installed package can be loaded from temporary > location > > > ** testing if installed package can be loaded from final location > > > ** testing if installed package keeps a record of temporary > > installation > > > path > > > * DONE (chimeraviz) > > > > > > Under: > > > > > >> sessionInfo() > > > R version 4.0.0 RC (2020-04-18 r78249) > > > Platform: x86_64-apple-darwin17.0 (64-bit) > > > Running under: macOS Catalina 10.15.3 > > > > > > Matrix products: default > > > BLAS: > > > > > > /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib > > > LAPACK: > > > > > > /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib > > > > > > locale: > > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods > base > > > > > > loaded via a namespace (and not attached): > > > [1] compiler_4.0.0 tools_4.0.0 > > > > > > The vignette looks okay as far as I can tell. > > > > > > -Kylie > > > > > > > > > > > > > > > > > > > > >> On Apr 24, 2020, at 1:40 AM, Hervé Pagès > <mailto:hpa...@fredhutch.org> > > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>>> > wrote: > > >> > > >> Interesting indeed. Thanks for checking this. > > >> > > >> Even though I'm not sure what conclusion to draw from all this. > >
Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz
t.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DiIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU%26s%3DitZMZz7G1z4hEn_h6m-WLnSXgIbD-41KOovzdseVHT4%26e%3Ddata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=zcOG%2BEG%2Bk16OXD2SN6pCGrZrQX8Rpwpx07gqYuBGPBE%3Dreserved=0
> >>>>> <
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fkuwisdelu.github.io-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DiIfSQOsSomvKm-5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2526s-253DitZMZz7G1z4hEn-5Fh6m-2DWLnSXgIbD-2D41KOovzdseVHT4-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C63723308658074-26amp-3Bsdata-3D9TmRy1lpNBJjGLZcqPqJY-252BMP32z2kgbsmTdvSn4RUk8-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DhNiYK5Qxom3Q8JMAgB15vH_K86oAT1s-ZFy1NFMtBcw%26e%3Ddata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421sdata=F9edg0Pf5jT9RZGC8B%2FIxJvV4DpW8Ztv3ZUDkw06tcs%3Dreserved=0
> >>
> >>>>>> On Apr 23, 2020, at 11:28 PM, Hervé Pagès >>>>>> <mailto:hpa...@fredhutch.org> <mailto:hpa...@fredhutch.org>> wrote:
> >>>>>>
> >>>>>> Ok so I'm changing my mind about this. I suspect that the error is
> >>>>>> actually related to the warning. The error comes from the magick
> >>>>>> package (a wrapper around the ImageMagick software) and it
> >>>>>> indicates a failure to crop an empty image. It can easily be
> >>>>>> reproduced with:
> >>>>>>
> >>>>>> ## Generate an empty image.
> >>>>>> png("myplot.png", bg="transparent")
> >>>>>> plot.new()
> >>>>>> dev.off()
> >>>>>>
> >>>>>> ## Try to crop it.
> >>>>>> magick::image_trim(magick::image_read("myplot.png"))
> >>>>>> # Error in magick_image_trim(image, fuzz) :
> >>>>>> # R: GeometryDoesNotContainImage `/Users/biocbuild/myplot.png'
> >>>>>> @ # warning/attribute.c/GetImageBoundingBox/247
> >>>>>>
> >>>>>> So I suspect that what happens is that the images generated on Mac
> >>>>>> by the code in the vignette are empty (because of the
> >>>>>> semi-transparency problem on Mac) which would explain why later
> >>>>>> knitr fails to crop them (it uses magick::image_trim() for that).
> >>>>>>
> >>>>>> I don't exactly understand why we wouldn't have seen the problem
> >>>>>> on merida1 though (same version of knitr (1.28) and magick (2.3)
> >>>>>> on both machines) but it seems that chimeraviz has changed
> >>>>>> significantly between BioC 3.10 and 3.11. Did you start using
> >>>>>> semi-transparency recently in your plots?
> >>>>>>
> >>>>>> Best,
> >>>>>> H.
> >>>>>>
> >>>>>>
> >>>>>> On 4/23/20 19:42, Hervé Pagès wrote:
> >>>>>>> Hi Stian,
> >>>>>>> I went on machv2 and gave this a shot. I can reproduce the
> >>>>>>> GeometryDoesNotContainImage error in an interactive session. I
> >>>>>>> don't have an answer yet but I was curious about the
> >>>>>>> "semi-transparency is not supported on this device" warning and
> >>>>>>> was wondering if it could somehow be related with the error.
> >>>>>>> It turns out that the warning is actually easy to reproduce on a
> >>>>>>> Mac with something like this:
> >>>>>>> plot.new()
> >>>>>>> lines(c(0.1, 0.22), c(0.5, 0.44), type = "l", lwd = 1, col =
> >>>>>>> "#FF80")
> >&
Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz
I'm still unable to reproduce this error on my end. If anyone with a mac could try building locally I would be very grateful. Thanks. On Sat, Apr 18, 2020 at 4:06 PM Stian Lågstad wrote: > Hi, > > I'm haven't been able to figure out this error for the latest machv2 build > for chimeraviz: > > ``` > Warning in doTryCatch(return(expr), name, parentenv, handler) : > semi-transparency is not supported on this device: reported only once > per page > Quitting from lines 108-126 (chimeraviz-vignette.Rmd) > Error: processing vignette 'chimeraviz-vignette.Rmd' failed with > diagnostics: > R: GeometryDoesNotContainImage > `/private/tmp/RtmpdBrrvk/Rbuild9ed5154894cc/chimeraviz/vignettes/chimeraviz-vignette_files/figure-html/unnamed-chunk-7-1.png' > @ warning/attribute.c/GetImageBoundingBox/247 > --- failed re-building ‘chimeraviz-vignette.Rmd’ > ``` > > The build in question: > http://bioconductor.org/checkResults/3.11/bioc-LATEST/chimeraviz/machv2-buildsrc.html > > If anyone has seen something like this before then I'd appreciate some > help. Thank you! > > -- > Stian Lågstad > +47 41 80 80 25 > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Change citation reference
Hi Federico, I believe you need to update the package version (in the DESCRIPTION file) to trigger a new build for those changes to be visible. If you update the version and push that change then a new build will be triggered. I see from http://bioconductor.org/checkResults/3.10/bioc-LATEST/ (search for "vulcan" there) that your package was last built: > Last Commit: b5638d5 > Last Changed Date: 2019-10-29 13:10:48 -0500 On Thu, Feb 27, 2020 at 3:19 PM Federico Giorgi wrote: > Dear all, > > I would like to change the citation in the vulcan package. > > https://bioconductor.org/packages/release/bioc/html/vulcan.html > > I have changed the reference in the inst/CITATION file within the package a > few weeks ago, but the old citation remains, even in the development > version: > https://bioconductor.org/packages/devel/bioc/html/vulcan.html > > Should I wait or is there another way to update the citation reference? > > Thanks, > > Federico > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure
prettyunits_1.0.2 > [21] bit_1.1-14 curl_4.2 > [23] compiler_3.6.0 htmlTable_1.13.2 > [25] DelayedArray_0.11.6 rtracklayer_1.45.6 > [27] scales_1.0.0checkmate_1.9.4 > [29] askpass_1.1 RCircos_1.2.1 > [31] rappdirs_0.3.1 stringr_1.4.0 > [33] digest_0.6.21 Rsamtools_2.1.6 > [35] foreign_0.8-72 rmarkdown_1.16 > [37] base64enc_0.1-3 dichromat_2.0-0 > [39] pkgconfig_2.0.3 htmltools_0.3.6 > [41] dbplyr_1.4.2BSgenome_1.53.2 > [43] htmlwidgets_1.3 rlang_0.4.0 > [45] rstudioapi_0.10 RSQLite_2.1.2 > [47] BiocParallel_1.19.3 acepack_1.4.1 > [49] dplyr_0.8.3 VariantAnnotation_1.31.4 > [51] RCurl_1.95-4.12 magrittr_1.5 > [53] GenomeInfoDbData_1.2.1 Formula_1.2-3 > [55] Matrix_1.2-17 Rcpp_1.0.2 > [57] munsell_0.5.0 yaml_2.2.0 > [59] stringi_1.4.3 SummarizedExperiment_1.15.9 > [61] zlibbioc_1.31.0 plyr_1.8.4 > [63] org.Hs.eg.db_3.8.2 BiocFileCache_1.9.1 > [65] blob_1.2.0 crayon_1.3.4 > [67] lattice_0.20-38 splines_3.6.0 > [69] hms_0.5.1 zeallot_0.1.0 > [71] knitr_1.25 pillar_1.4.2 > [73] biomaRt_2.41.8 XML_3.98-1.20 > [75] glue_1.3.1 evaluate_0.14 > [77] biovizBase_1.33.1 latticeExtra_0.6-28 > [79] BiocManager_1.30.4 vctrs_0.2.0 > [81] org.Mm.eg.db_3.8.2 gtable_0.3.0 > [83] openssl_1.4.1 purrr_0.3.2 > [85] assertthat_0.2.1ggplot2_3.2.1 > [87] xfun_0.10 ArgumentCheck_0.10.2 > [89] survival_2.44-1.1 tibble_2.1.3 > [91] GenomicAlignments_1.21.7memoise_1.1.0 > [93] cluster_2.1.0 BiocStyle_2.13.2 > > On 10/2/19 11:27, Stian Lågstad wrote: > > Hi, > > > > The most recent build of chimeraviz fails when rebuilding the vignette: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_chimeraviz_malbec1-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=UJ6fJMh-a_gWEyrhxw-8R4NRmxLgBEwS5BAsWho6xEU=AJDC2yvC23fZff7t5a-pwOsxPLZZJVMo614bEkL5lHY= > , > > and I'm unable to reproduce this locally. Does anyone have ideas as to > how > > I can dig deeper into this? > > > > Thank you. > > > > Here's an excerpt from build log in case it disappears when the new build > > is done: > > ``` > > Quitting from lines 564-591 (chimeraviz-vignette.Rmd) > > Error: processing vignette 'chimeraviz-vignette.Rmd' failed with > > diagnostics: > > trying to set zero length metadata columns on a non-zero length > >object > > --- failed re-building ‘chimeraviz-vignette.Rmd’ > > > > SUMMARY: processing the following file failed: > >‘chimeraviz-vignette.Rmd’ > > > > Error: Vignette re-building failed. > > Execution halted > > ``` > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure
Hi, The most recent build of chimeraviz fails when rebuilding the vignette: https://bioconductor.org/checkResults/3.10/bioc-LATEST/chimeraviz/malbec1-buildsrc.html, and I'm unable to reproduce this locally. Does anyone have ideas as to how I can dig deeper into this? Thank you. Here's an excerpt from build log in case it disappears when the new build is done: ``` Quitting from lines 564-591 (chimeraviz-vignette.Rmd) Error: processing vignette 'chimeraviz-vignette.Rmd' failed with diagnostics: trying to set zero length metadata columns on a non-zero length object --- failed re-building ‘chimeraviz-vignette.Rmd’ SUMMARY: processing the following file failed: ‘chimeraviz-vignette.Rmd’ Error: Vignette re-building failed. Execution halted ``` -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Unable to reproduce chimeraviz 3.9 build failure (test failure)
Hi,
The most recent build of chimeraviz failed due to a test failure:
https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/chimeraviz/malbec2-checksrc.html.
That the test in question should suddenly fail surprises me, and I'm unable
to reproduce this locally. Does anyone have ideas as to how I can dig
deeper into this?
Thank you!
Here's an excerpt from build log in case it disappears when the new build
is done:
```
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
>
> test_check("chimeraviz")
── 1. Failure: get_ensembl_ids gets the correct Ensembl gene ids for a
fusion ob
fusion@gene_upstream@ensembl_id not equal to
`correct_ensembl_id_upstream`.
Lengths differ: 2 is not 1
══ testthat results
═══
OK: 170 SKIPPED: 0 FAILED: 1
1. Failure: get_ensembl_ids gets the correct Ensembl gene ids for a
fusion object (@test_utilities.R#217)
Error: testthat unit tests failed
```
--
Stian Lågstad
+47 41 80 80 25
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`
I usually create a seperate branch for work, which I merge into master when I'm happy with the result. Will that be a problem? Should I rebase instead to avoid it? Thank you. On Wed, Jan 17, 2018 at 6:48 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi Stian, > > I’ve enabled you to push to your repository on Bioconductor. > > Your duplicate commit history weaves in and out because of merges along > the way from your GitHub repository. At this point, there is very little I > can do to help unless I spend a lot of time on your package, manually > fixing the history. > > The duplicate commits should not effect your package development, and you > should continue with it. It does not effect the build process as well. > > If you feel like this is something you can fix from your end, by using > “git reset” and “git cherry-pick” you should feel free to fix. Let me know > when you are successful, and I can help you push the updated repo. > > For the future, duplicate commits are caused by “merge” commands. You > might want to search for those if you want to know which commits are > causing these duplicates. > > Best, > > Nitesh > > > > On Jan 13, 2018, at 8:36 PM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org> wrote: > > > > Hi Stian, > > > > I’m looking into it. Your commit history seems to have a discontinuous > history of duplicates + non-duplicates caused by merge from different > sources. I’m yet to figure out how to solve this situation. > > > > I will get back to you within a couple of days. > > > > Best, > > > > Nitesh > > > > > >> On Jan 13, 2018, at 12:35 PM, Stian Lågstad <stianlags...@gmail.com> > wrote: > >> > >> Hi, > >> > >> Could someone help me get past the duplicate commits error? I'm not sure > >> what to do. > >> > >> These are the steps I've taken: > >> > >> 1. Clone the repository. `git clone g...@git.bioconductor.org:packa > >> ges/chimeraviz` > >> 2. Make a small change in master + attempt to push it, and got this: > >> ``` > >> ➜ chimeraviz-bioconductor git:(master) git push > >> > >> Counting objects: 4, done. > >> Delta compression using up to 8 threads. > >> Compressing objects: 100% (4/4), done. > >> Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done. > >> > >> Total 4 (delta 3), reused 0 (delta 0) > >> remote: Error: duplicate commits. > >> remote: > >> remote: There are duplicate commits in your commit history, These > cannot be > >> remote: pushed to the Bioconductor git server. Please make sure that > this is > >> remote: resolved. > >> remote: > >> remote: Take a look at the documentation to fix this, > >> remote: https://bioconductor.org/developers/how-to/git/sync- > >> existing-repositories/, > >> remote: particularly, point #8 (force Bioconductor master to Github > master). > >> remote: > >> remote: For more information, or help resolving this issue, contact > >> remote: <bioc-devel@r-project.org>. Provide the error, the package > name and > >> remote: any other details we might need. > >> remote: > >> remote: Use > >> remote: > >> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b > >> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2 > >> remote: > >> remote: to see body of commits. > >> remote: > >> To g...@git.bioconductor.org:packages/chimeraviz > >> > >> ! [remote rejected] master -> master (pre-receive hook declined) > >> ``` > >> > >> I do see what looks like duplicate commits in the git log. For > >> example ba964db26ac49e86a5374e0dc3040769ae799113 > >> and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat > Apr 8 > >> 17:45:42 2017. But I've been successful in making changes after april > last > >> year. > >> > >> -- > >> Stian Lågstad > >> +47 41 80 80 25 > >> > >> [[alternative HTML version deleted]] > >> > >> ___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s)
[Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`
Hi, Could someone help me get past the duplicate commits error? I'm not sure what to do. These are the steps I've taken: 1. Clone the repository. `git clone g...@git.bioconductor.org:packa ges/chimeraviz` 2. Make a small change in master + attempt to push it, and got this: ``` ➜ chimeraviz-bioconductor git:(master) git push Counting objects: 4, done. Delta compression using up to 8 threads. Compressing objects: 100% (4/4), done. Writing objects: 100% (4/4), 422 bytes | 0 bytes/s, done. Total 4 (delta 3), reused 0 (delta 0) remote: Error: duplicate commits. remote: remote: There are duplicate commits in your commit history, These cannot be remote: pushed to the Bioconductor git server. Please make sure that this is remote: resolved. remote: remote: Take a look at the documentation to fix this, remote: https://bioconductor.org/developers/how-to/git/sync- existing-repositories/, remote: particularly, point #8 (force Bioconductor master to Github master). remote: remote: For more information, or help resolving this issue, contact remote: <bioc-devel@r-project.org>. Provide the error, the package name and remote: any other details we might need. remote: remote: Use remote: remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2 remote: remote: to see body of commits. remote: To g...@git.bioconductor.org:packages/chimeraviz ! [remote rejected] master -> master (pre-receive hook declined) ``` I do see what looks like duplicate commits in the git log. For example ba964db26ac49e86a5374e0dc3040769ae799113 and 8a49e3cdd1ce5257879d752aeead83813c6a4044, which are both from Sat Apr 8 17:45:42 2017. But I've been successful in making changes after april last year. -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor Git: Online interface
I would very much appreciate this as well. Issue tracking and communicating with users directly in the repository would be very nice, as well as the ability to reference source code directly. On Thu, Oct 26, 2017 at 8:50 AM, Henrik Bengtsson < henrik.bengts...@gmail.com> wrote: > Are there any plans for an online interface to > https://git.bioconductor.org/? > > I've recently looked into solutions for an open-source in-house > "GitHub/GitLab"-ish, and I've found https://gitea.io/ to be really > nice. It is very easy to install. It has support for various common > user authentication methods, it supports organizations and user teams, > repositories may have issues and wikis, sets of code lines can be > referenced, commits and code diffs are annotated, and so on. Wikis > and issue trackers can be disabled (also for individual repositories). > That's all I've learned thus far - I'm impressed. > > Just a thought > > Henrik > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Install directly from the bioconductor git repo?
Thank you Martin. Are the core packages being kept as Github mirrors?
On Wed, Oct 25, 2017 at 3:21 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 10/24/2017 04:16 PM, Stian Lågstad wrote:
>
>> Can I install a package directly from a Bioconductor git repository? Like
>> I
>> can for example using devtools and a github repository like this:
>> `install_git("git://github.com/hadley/stringr.git")`? What would be the
>> link for a Bioconductor package?
>>
>
> install_git("https://git.bioconductor.org/packages/BiocGenerics.git;)
>
> seems to work.
>
>
>> Also, can I link directly to a source code file somehow? Like I can with
>> the github repository:
>> https://github.com/tidyverse/stringr/blob/master/R/case.R#L21
>>
>
> no, not at the moment, except of course for packages that are mirrored on
> github
>
> https://github.com/Bioconductor/BiocGenerics/blob/master/DESCRIPTION#L4
>
> Martin
>
>
>> Thank you.
>>
>>
>
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[Bioc-devel] Package missing from the latest build report?
I've recently pushed some changes to chimeraviz ( https://bioconductor.org/packages/devel/bioc/html/chimeraviz.html) and I was waiting to see that the next build turned out alright, but now it looks like chimeraviz is missing from the list at http://bioconductor.org/checkResults/devel/bioc-LATEST/. Could that be because I pushed changes right when the snapshot was taken, or is there another reason? -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor 3.6 release: update NEWS
Hi, What should the NEWS file look like? Are there guidelines somewhere? Also, where should it be located? This page <https://www.bioconductor.org/developers/package-submission/> says `inst/NEWS`, but I see many packages has the file at root level. On Fri, Oct 13, 2017 at 5:16 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Package maintainers, > > If you haven't already, please update the NEWS files in your packages. > This information will be included in the release announcement. The deadline > for updating NEWS files is Tuesday, October 24: > > http://www.bioconductor.org/developers/release-schedule/ > > Thanks. > > Valerie > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] How can I fetch the release-3.5 branch?
Hi, Congratulations on the release! Now that my package has moved from just being in devel and now also being in release: How can I fetch the release branch? To show you what my local system looks like now: """ ➜ chimeraviz git:(master) git branch devel * master ➜ chimeraviz git:(master) git branch -a devel * master remotes/bioc/master remotes/git-svn-devel remotes/origin/master ➜ chimeraviz git:(master) cat .git/config [core] repositoryformatversion = 0 filemode = true bare = false logallrefupdates = true [remote "origin"] url = g...@github.com:stianlagstad/chimeraviz.git fetch = +refs/heads/*:refs/remotes/origin/* [branch "master"] remote = origin merge = refs/heads/master [remote "bioc"] url = https://github.com/Bioconductor-mirror/chimeraviz.git fetch = +refs/heads/*:refs/remotes/bioc/* [svn-remote "devel"] url = https://hedgehog.fhcrc.org/bioconductor//trunk/madman/Rpacks/chimeraviz fetch = :refs/remotes/git-svn-devel [branch "devel"] remote = bioc merge = refs/heads/master """ Do I have to add something like "[svn-remote "release-3.5"]" to the config? Thank you. -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor 3.5 release: April 7 deadlines
I've added a new function to my package chimeraviz (so far it's in a separate branch and not commited to Bioconductor). Does the API freeze mean that I have to wait until the Bioconductor release before I commit it to the devel branch? On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain <voben...@gmail.com> wrote: > Hi, > > Some recent activity has caused some (red) ripples across the builds and > the El Capitan Mac builds are still unsettled. To accommodate, we're > extending the deadline to pass R CMD build and check with no errors to next > Friday (http://www.bioconductor.org/developers/release-schedule/). Thanks > to everyone for cleaning up their packages and communicating problems (and > solutions!) on the lists. > > Key deadlines for April 7 are > > - No new packages added to the 3.5 roster > > - No more API changes > > - Current release 3.4 builds will stop > > - Annotation packages (both internal and contributed) posted to the 3.5 > repo > > Valerie > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter
How does the error deadline tomorrow (http://www.bioconductor.org/ developers/release-schedule/) affect packages that are still red because of this change? I don't know what else to do other than to wait for changes in Gviz (which my package is dependent on). Thanks. On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > Sorry I have been traveling. Will get to it soon. > > On Apr 4, 2017 12:58 PM, "Rainer Johannes" <johannes.rai...@eurac.edu> > wrote: > > > Hi Herve, > > > > sorry for all the reds - actually I provided the patches to biovizBase > and > > ggbio, but it did not work out that smoothly that I hoped. For the other > > packages that depend on ensembldb there's no problem or only small > changes > > required (did contact the developers). > > Fingers crossed that Michael can patch biovizBase and ggbio soon. > > > > cheers, jo > > > > > On 4 Apr 2017, at 21:34, Hervé Pagès <hpa...@fredhutch.org> wrote: > > > > > > Hi Johannes, > > > > > > This move is generating a lot of red today on the build report. > > > Hopefully biovizBase and ggbio can be fixed quickly. Note that > > > maybe a smoother path would have been to notify the maintainers > > > of these packages first and wait that they make the required > > > changes (i.e. to import the filters from AnnotationFilter) > > > before modifying ensembldb. Maybe for next time ;-) > > > > > > Cheers, > > > H. > > > > > > On 04/04/2017 04:02 AM, Rainer Johannes wrote: > > >> > > >> > > >> On 4 Apr 2017, at 10:59, Stian Lågstad <stianlags...@gmail.com : > > stianlags...@gmail.com>> wrote: > > >> > > >> Hi, > > >> > > >> Thanks again for notifying me about the changes needed in chimeraviz. > > Right now I'm having problems installing Gviz - I get these errors: > > >> > > >> """ > > >> No methods found in "GenomicAlignments" for requests: > > pmapFromTranscripts > > >> Error : object 'GRangesFilter' is not exported by > 'namespace:ensembldb' > > >> ERROR: lazy loading failed for package 'Gviz' > > >> """ > > >> > > >> Are these errors caused by the change in ensembldb? If so: Do you know > > how I can keep developing without having to wait for Gviz? > > >> > > >> > > >> These come from biovizBase which Gviz imports. I've sent Micheal the > > fixes for biovizBase and ggbio that should fix this. > > >> We need to wait for the changes to be propagated, since also for > > ensembldb I get today still version 1.99.12 but not the new 1.99.13. > > >> > > >> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes < > > johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu>> wrote: > > >> Dear all, > > >> > > >> I've just committed a change in ensembldb (version 1.99.13) that > > removes all filter classes from it and imports them from the > > AnnotationFilter package. This change will break biovizBase and ggbio > (and > > all packages downstream of them, e.g. Gviz). I've already sent Michael > > Lawrence patches to fix both packages, but there might still be some > > problems in the upcoming build reports I guess. > > >> > > >> I've also contacted the developers of the TVTB and chimeraviz packages > > and made them aware of the change. Could be that there are other packages > > out there possibly affected by the change. If so, let me know and I'll > > assist fixing the problems (if needed). > > >> > > >> cheers, jo > > >> > > >> ___ > > >> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing > list > > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAf > qt84VtBcfhQ= > > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy- > > PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY= > > >> > > >> > > >> > > >> -- > > >> Stian Lågstad > > >> +47 41 80 80 25 > > >> > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> ___ > > >> Bioc-devel@r-project.org mailing list > > >>
Re: [Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?
Thank you both. Could you also advice me on the error I'm receiving on oaxaca? "there is no package called 'webshot'" New build report: http://bioconductor.org/spb_reports/chimeraviz_ buildreport_20161207152203.html On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Stian, > > The build machines used by the SPB are the same as the machines used > for the daily builds and they already have the latest BiocStyle > installed (BiocStyle 2.3.23). You can see this by going on the daily > build report for devel and clicking on any of the link in the > "Installed pkgs" column in the top table: > > https://bioconductor.org/checkResults/3.5/bioc-LATEST/ > > However, the SPB report for your package is from Nov 30 so it could > be that it predates the fix in BiocStyle. You can trigger a new build > of your package by just bumping its version on github. > > Hope this helps, > H. > > > On 12/07/2016 07:17 AM, Leonardo Collado Torres wrote: > >> Hi Stian, >> >> Install BiocStyle 2.3.20 or newer and that error will go away. See >> https://github.com/Bioconductor/BiocStyle/issues/20 for details. >> >> Best, >> Leo >> >> On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad <stianlags...@gmail.com> >> wrote: >> >>> Hi, >>> >>> Could someone please advice me on the errors I'm getting building my >>> package? I'm unable to reproduce them locally. >>> >>> Link to build report: >>> http://bioconductor.org/spb_reports/chimeraviz_buildreport_ >>> 20161130173413.html >>> Link to bioconductor submission issue: >>> https://github.com/Bioconductor/Contributions/issues/206 >>> >>> I'm getting an error on creating my vignette: `argumemt is not a >>> character >>> vector` >>> I also get this: `there is no package called 'webshot'` >>> >>> I believe these could be related to this warning: `Warning in >>> engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) >>> and/or pandoc-citeproc not available. Falling back to R Markdown v1.` >>> >>> I use rmarkdown_1.2 locally without problems. Can someone here assist me? >>> >>> Thank you. >>> >>> -- >>> Stian Lågstad >>> +47 41 80 80 25 >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?
Hi, Could someone please advice me on the errors I'm getting building my package? I'm unable to reproduce them locally. Link to build report: http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html Link to bioconductor submission issue: https://github.com/Bioconductor/Contributions/issues/206 I'm getting an error on creating my vignette: `argumemt is not a character vector` I also get this: `there is no package called 'webshot'` I believe these could be related to this warning: `Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.` I use rmarkdown_1.2 locally without problems. Can someone here assist me? Thank you. -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
